LAMMPS cylindrical wall/srd

# 3d srd in a cylinder with gravity acting along it, starting from stationary

units		lj
atom_style	atomic
atom_modify	first empty
dimension	3
boundary	f f p

# set simulation size variables

variable xlength equal 10
variable ylength equal 10
variable zlength equal 10

variable x0 equal v_xlength/2
variable y0 equal v_ylength/2

variable radius equal 4.5

variable WallSRDxlo equal v_x0-sqrt(v_radius*v_radius-(y-v_y0)*(y-v_y0))
variable WallSRDxhi equal v_x0+sqrt(v_radius*v_radius-(y-v_y0)*(y-v_y0))
variable WallSRDylo equal v_y0-sqrt(v_radius*v_radius-(x-v_x0)*(x-v_x0))
variable WallSRDyhi equal v_y0+sqrt(v_radius*v_radius-(x-v_x0)*(x-v_x0))

# create box with big lattice

lattice		sc 0.4
region		box block 0 10 0 10 0 10
create_box	1 box

#print "${WallSRDxlo} ${WallSRDxhi} ${WallSRDylo} ${WallSRDyhi}"

# create cylinder along z-axis across sim box, centre at x=5,y=5, radius 4

region		tube cylinder z 5 5 4 EDGE EDGE side in

# add SRD particles as hi density lattice

lattice		sc 250.0
create_atoms	1 region tube

group		srdparticles type 1
group		empty type 2

mass		1 0.01
velocity	all create 1.0 593849 loop geom

# settings - need dummy empty group to enable no communication

neighbor	0.3 bin
neigh_modify	delay 1 every 1 check no

communicate	single group empty

# timestep is big and SRD frequency is 1

timestep	0.02

fix	        1 all srd 1 NULL 1.0 0.3 49894 &
		  collision noslip overlap yes inside ignore
fix		2 all gravity 1.0 vector 0 0 1
#fix		3 all wall/region tubewall lj126 1 1 0.5
#fix		4 all wall/srd xlo 0.5 xhi 9.5 ylo 0.5 yhi 9.5
fix		4 all wall/srd &
		xlo WallSRDxlo 	xhi WallSRDxhi &
		ylo WallSRDylo 	yhi WallSRDyhi

# diagnostics

#thermo_style	custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
#thermo		100
thermo_modify	lost warn
#dump		1 all atom 250 dump.srd.pure.cylinder
#dump		1 all custom 1 dump.srd.pure.cylinder id x y z vx vy vz
dump		1 all atom 1 dump.srd.pure.cylinder

#dump_modify	1 format "%d %12.8g %12.8g %12.8g %12.8g %12.8g %12.8g"

run		200
#run		5000